In absence of arabinose, AraC binds to
Without L-arabinose, AraC apoprotein adopts conformation strongly promoting looping-mediated repression of araBAD operon. Dimer bridges high-affinity araO2 site centered approximately minus 280 upstream and araI1 site at minus 106, with intervening 210 base pairs bent into looped architecture demonstrated by electron microscopy. Crystallographic studies show N-terminal arms dimerize antiparallel, stabilizing loop topology. Looped conformation buries PBAD minus35 promoter element and occludes CAP-cAMP binding site, preventing RNA polymerase holoenzyme initiation. Approximately twenty AraC molecules per bacterial cell suffice to maintain tight repression, ensuring low basal expression until arabinose reaches threshold concentration sufficient to disrupt loop architecture.
Ref: Science DNA Looping by AraC – apo-AraC prefers looping between araO2 and araI1 repressing araBAD.